Validation Report - circlize@0.4.16
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package circlize
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 113 |
| has_vignettes | 2 |
| export_help | 113 |
| has_website | TRUE |
| has_maintainer | Zuguang Gu z.gu@dkfz.de |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_source_control | https://github.com/jokergoo/circlize |
| has_bug_reports_url | 0 |
| downloads_1yr | 396656 |
| reverse_dependencies | 157 |
| has_examples | 1 |
| dependencies | 9 |
| license | MIT + file LICENSE |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | graphics | Depends |
| 2 | GlobalOptions (>= 0.1.2) | Imports |
| 3 | shape | Imports |
| 4 | grDevices | Imports |
| 5 | utils | Imports |
| 6 | stats | Imports |
| 7 | colorspace | Imports |
| 8 | methods | Imports |
| 9 | grid | Imports |
Package dependencies
Reverse dependencies
Overall the package has 157 reverse dependencies:
abseqR, acc, AMARETTO, artMS, ASURAT, avidaR, bambu, bandle, barcodetrackR, BasketballAnalyzeR, BeeBDC, bettr, bfw, blacksheepr, BloodGen3Module, bulkAnalyseR, canceR, capm, CATALYST, CCPlotR, celda, CeTF, CHRONOS, CIARA, CINNA, ClustAll, ClusterGVis, CNVScope, coda4microbiome, cola, comapr, ComplexHeatmap, corrViz, COTAN, countToFPKM, CRISPRball, CTexploreR, cytoKernel, dcanr, DEGreport, dendextend, DEP, DEploid.utils, DEsubs, diffcyt, dinoR, dominoSignal, eclust, ELMER, EnrichedHeatmap, epiregulon.extra, ethnobotanyR, FLAMES, ForecastTB, GALLO, gap, GeDi, GeneTonic, GenomicPlot, GenomicSuperSignature, gfer, gINTomics, gmoviz, grandR, GRaNIE, GRIN2, GSSTDA, gtrellis, hermes, HilbertCurve, hoodscanR, immunarch, inferCSN, InteractiveComplexHeatmap, InterCellar, ISAnalytics, iSEE, ITNr, karyotapR, LymphoSeq, MAPFX, martini, MesKit, MetaNet, metasnf, MetCirc, miaViz, migest, MiscMetabar, missoNet, MitoHEAR, MKomics, mldr, MOMA, monaLisa, Moonlight2R, MoonlightR, MOSClip, multistateQTL, nipalsMCIA, OpenLand, pareg, pathlinkR, pathwayPCA, pcutils, PeacoQC, pgxRpi, PhosR, pipeComp, Platypus, plotthis, PolySTest, profileplyr, PRONE, ProtE, recoup, RepertoiR, rexposome, rGREAT, rKOMICS, rliger, RNAseqQC, RPointCloud, RVA, scCustomize, scDblFinder, scITD, SCpubr, scRepertoire, scRNAseqApp, sechm, seewave, SEtools, sigminer, sigQC, simona, simplifyEnrichment, SingleCellSignalR, singleCellTK, socialh, SpaCCI, sparrow, spiralize, svaNUMT, svaRetro, TBSignatureProfiler, TCGAbiolinks, tidyHeatmap, tinyarray, TMSig, TransProR, TRONCO, viscomp, visxhclust, wilson, YAPSA, yarrr
Namespace
Overall the package has 113 exported objects. 113 are documented:
$.CELL_META add_transparency
TRUE TRUE
adjacencyList2Matrix adjacencyMatrix2List
TRUE TRUE
arrange_links_evenly calc_gap
TRUE TRUE
CELL_META chordDiagram
TRUE TRUE
chordDiagramFromDataFrame chordDiagramFromMatrix
TRUE TRUE
circlize circos.arrow
TRUE TRUE
circos.axis circos.barplot
TRUE TRUE
circos.boxplot circos.clear
TRUE TRUE
circos.connect circos.dendrogram
TRUE TRUE
circos.genomicAxis circos.genomicDensity
TRUE TRUE
circos.genomicHeatmap circos.genomicIdeogram
TRUE TRUE
circos.genomicInitialize circos.genomicLabels
TRUE TRUE
circos.genomicLines circos.genomicLink
TRUE TRUE
circos.genomicPoints circos.genomicPosTransformLines
TRUE TRUE
circos.genomicRainfall circos.genomicRect
TRUE TRUE
circos.genomicText circos.genomicTrack
TRUE TRUE
circos.genomicTrackPlotRegion circos.heatmap
TRUE TRUE
circos.heatmap.initialize circos.heatmap.link
TRUE TRUE
circos.info circos.initialize
TRUE TRUE
circos.initializeCircularGenome circos.initializeWithIdeogram
TRUE TRUE
circos.labels circos.lines
TRUE TRUE
circos.link circos.nested
TRUE TRUE
circos.par circos.points
TRUE TRUE
circos.polygon circos.raster
TRUE TRUE
circos.rect circos.segments
TRUE TRUE
circos.text circos.track
TRUE TRUE
circos.trackHist circos.trackLines
TRUE TRUE
circos.trackPlotRegion circos.trackPoints
TRUE TRUE
circos.trackText circos.triangle
TRUE TRUE
circos.update circos.updatePlotRegion
TRUE TRUE
circos.violin circos.xaxis
TRUE TRUE
circos.yaxis cm_h
TRUE TRUE
cm_x cm_y
TRUE TRUE
col2value colorRamp2
TRUE TRUE
convert_height convert_length
TRUE TRUE
convert_x convert_y
TRUE TRUE
cytoband.col degree
TRUE TRUE
draw.sector fontsize
TRUE TRUE
generateRandomBed genomicDensity
TRUE TRUE
get_most_inside_radius get.all.sector.index
TRUE TRUE
get.all.track.index get.cell.meta.data
TRUE TRUE
get.current.chromosome get.current.sector.index
TRUE TRUE
get.current.track.index getI
TRUE TRUE
highlight.chromosome highlight.sector
TRUE TRUE
inch_h inch_x
TRUE TRUE
inch_y inches_h
TRUE TRUE
inches_x inches_y
TRUE TRUE
mm_h mm_x
TRUE TRUE
mm_y names.CELL_META
TRUE TRUE
posTransform.default posTransform.text
TRUE TRUE
print.CELL_META rainfallTransform
TRUE TRUE
rand_color read.chromInfo
TRUE TRUE
read.cytoband reverse.circlize
TRUE TRUE
set_track_gap set.current.cell
TRUE TRUE
show.index smartAlign
TRUE TRUE
uh ux
TRUE TRUE
uy
TRUE Examples
There are 112 help pages with examples, from 112 (100.00 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-16 04:21:09 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.2 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.49 jsonlite_1.8.9
[10] xfun_0.50 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
_R_CHECK_SYSTEM_CLOCK_
FALSE
ACCEPT_EULA Y
ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE
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ANDROID_SDK_ROOT /usr/local/lib/android/sdk
ANT_HOME /usr/share/ant
AZURE_EXTENSION_DIR /opt/az/azcliextensions
BOOTSTRAP_HASKELL_NONINTERACTIVE
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GITHUB_TRIGGERING_ACTOR
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HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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LN_S ln -s
LOGGER_LOG_LEVEL DEBUG
MAKE make
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT 1000
PHARMAPKGS_PLATFORM ubuntu-22.04
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PHARMAPKGS_REMOTE_REPO
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PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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YES
PWD /home/runner/work/pharmapkgs/pharmapkgs
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QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_PATH /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE
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R_PLATFORM x86_64-pc-linux-gnu
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R_RD4PDF times,inconsolata,hyper
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R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RUNNER_ARCH X64
RUNNER_ENVIRONMENT github-hosted
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RUNNER_TEMP /home/runner/work/_temp
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RUNNER_TRACKING_ID github_d0120492-4873-4b13-9ede-fb6d0d82420b
RUNNER_USER runner
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SED /usr/bin/sed
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SGX_AESM_ADDR 1
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STATS_D true
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SWIFT_PATH /usr/share/swift/usr/bin
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TAR /usr/bin/tar
TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
/usr/local/share/vcpkg
XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
[1] TRUE
$bitmapType
[1] "cairo"
$browser
[1] "xdg-open"
$browserNLdisabled
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
{
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custom_handler(msg)
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else {
cli_server_default(msg)
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<bytecode: 0x55a3caabe910>
<environment: namespace:cli>
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$citation.bibtex.max
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$continue
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$contrasts
unordered ordered
"contr.treatment" "contr.poly"
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$demo.ask
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$deparse.cutoff
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$device
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{
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<bytecode: 0x55a3ca215b40>
<environment: namespace:knitr>
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$locatorBell
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$matprod
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$max.print
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$na.action
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$papersize
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$PCRE_limit_recursion
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$pdfviewer
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$pkgType
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$printcmd
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$prompt
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$repos
CRAN
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$rl_word_breaks
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$rlang_trace_top_env
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$scipen
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$show.coef.Pvalues
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$show.error.messages
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$show.signif.stars
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$showErrorCalls
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$showNCalls
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$str
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$str$digits.d
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$str$vec.len
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$str$list.len
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$str$deparse.lines
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$str$drop.deparse.attr
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$str$formatNum
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format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x55a3c9f96520>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
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mode "w+b"
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can write "yes"
$ts.eps
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$ts.S.compat
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$unzip
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$useFancyQuotes
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$warning.length
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$width
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